Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
to extract flanking regions for cloning. If the result of the multiple sequence alignment is
not as expected, these results could be used for further investigation.
qseqid
sseqid
percentage.identical
alignment.length
no.mismatch
no.gap.openings
qstart
qend
sstart
send
evalue
bitscore
0
TraesCS6A01G376900
chr6A
100.000
2555
0
0
1
2555
598462147
598459593
0.000000e+00
4682.0
1
TraesCS6A01G376900
chr6A
98.669
2555
16
1
1
2555
598328045
598325509
0.000000e+00
4514.0
2
TraesCS6A01G376900
chr6A
98.435
2556
21
3
1
2555
598254761
598252224
0.000000e+00
4481.0
3
TraesCS6A01G376900
chr6A
99.105
1899
16
1
658
2555
598569209
598567311
0.000000e+00
3411.0
4
TraesCS6A01G376900
chr6A
99.464
1867
9
1
690
2555
598521389
598519523
0.000000e+00
3391.0
5
TraesCS6A01G376900
chr6A
99.419
1032
6
0
1524
2555
598386926
598385895
0.000000e+00
1873.0
6
TraesCS6A01G376900
chr6A
96.400
861
13
1
1
861
598387769
598386927
0.000000e+00
1404.0
7
TraesCS6A01G376900
chr6A
98.361
549
9
0
1
549
598571097
598570549
0.000000e+00
965.0
8
TraesCS6A01G376900
chr6A
86.486
888
58
20
1000
1861
598576284
598575433
0.000000e+00
918.0
9
TraesCS6A01G376900
chr6A
90.521
211
15
3
2215
2423
598574110
598573903
9.010000e-70
274.0
10
TraesCS6A01G376900
chr6A
84.615
130
15
3
661
790
598213186
598213062
9.600000e-25
124.0
11
TraesCS6A01G376900
chrUn
98.080
1354
8
1
1
1354
341386533
341387868
0.000000e+00
2340.0
12
TraesCS6A01G376900
chr6B
78.784
1414
207
54
1071
2430
687413529
687412155
0.000000e+00
863.0
13
TraesCS6A01G376900
chr6B
86.422
545
32
12
1078
1580
687367125
687366581
2.220000e-155
558.0
14
TraesCS6A01G376900
chr6B
81.027
448
37
16
1664
2089
687371913
687371492
1.910000e-81
313.0
15
TraesCS6A01G376900
chr6B
77.248
545
79
21
1285
1797
687108628
687109159
6.960000e-71
278.0
16
TraesCS6A01G376900
chr6B
79.553
313
33
10
1285
1580
687317799
687317501
7.210000e-46
195.0
17
TraesCS6A01G376900
chr6B
83.756
197
9
4
1916
2089
687366206
687366010
5.660000e-37
165.0
18
TraesCS6A01G376900
chr6B
91.304
115
10
0
1623
1737
687366388
687366274
9.460000e-35
158.0
19
TraesCS6A01G376900
chr6B
93.939
66
4
0
786
851
687318432
687318367
1.620000e-17
100.0
20
TraesCS6A01G376900
chr6D
78.252
1407
181
65
1071
2430
452709767
452708439
0.000000e+00
787.0
21
TraesCS6A01G376900
chr6D
83.884
484
44
14
1285
1735
452641702
452641220
5.050000e-117
431.0
22
TraesCS6A01G376900
chr6D
91.093
247
22
0
1623
1869
452641234
452640988
4.070000e-88
335.0
23
TraesCS6A01G376900
chr6D
96.552
58
2
0
794
851
452642177
452642120
2.090000e-16
97.1
24
TraesCS6A01G376900
chr6D
92.424
66
5
0
786
851
452593440
452593375
7.530000e-16
95.3
25
TraesCS6A01G376900
chr6D
85.567
97
6
3
2001
2089
452640039
452639943
7.530000e-16
95.3
26
TraesCS6A01G376900
chr2A
76.759
469
99
9
23
485
637700977
637700513
1.170000e-63
254.0
27
TraesCS6A01G376900
chr4D
70.884
498
127
16
69
555
447890544
447891034
1.620000e-17
100.0
28
TraesCS6A01G376900
chr4D
79.200
125
23
3
69
191
425101725
425101602
1.630000e-12
84.2
29
TraesCS6A01G376900
chr4D
79.200
125
23
3
69
191
494019475
494019598
1.630000e-12
84.2
30
TraesCS6A01G376900
chr2D
71.053
418
111
9
69
480
589755093
589755506
2.710000e-15
93.5
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
purely upstream or downstream may be removed if they don't overlap both primers.
query
scaffold
start
end
length
rev.comp
avg.bitscore
max.bitscore
avg.percent.identical
query.start
query.end
num_hsp
groupid
homo_length
0
TraesCS6A01G376900
chr6A
598459593
598462147
2554
True
4682.000000
4682
100.000000
1
2555
1
chr6A.!!$R4
2554
1
TraesCS6A01G376900
chr6A
598325509
598328045
2536
True
4514.000000
4514
98.669000
1
2555
1
chr6A.!!$R3
2554
2
TraesCS6A01G376900
chr6A
598252224
598254761
2537
True
4481.000000
4481
98.435000
1
2555
1
chr6A.!!$R2
2554
3
TraesCS6A01G376900
chr6A
598519523
598521389
1866
True
3391.000000
3391
99.464000
690
2555
1
chr6A.!!$R5
1865
4
TraesCS6A01G376900
chr6A
598385895
598387769
1874
True
1638.500000
1873
97.909500
1
2555
2
chr6A.!!$R6
2554
5
TraesCS6A01G376900
chr6A
598567311
598576284
8973
True
1392.000000
3411
93.618250
1
2555
4
chr6A.!!$R7
2554
6
TraesCS6A01G376900
chrUn
341386533
341387868
1335
False
2340.000000
2340
98.080000
1
1354
1
chrUn.!!$F1
1353
7
TraesCS6A01G376900
chr6B
687412155
687413529
1374
True
863.000000
863
78.784000
1071
2430
1
chr6B.!!$R2
1359
8
TraesCS6A01G376900
chr6B
687366010
687367125
1115
True
293.666667
558
87.160667
1078
2089
3
chr6B.!!$R4
1011
9
TraesCS6A01G376900
chr6B
687108628
687109159
531
False
278.000000
278
77.248000
1285
1797
1
chr6B.!!$F1
512
10
TraesCS6A01G376900
chr6D
452708439
452709767
1328
True
787.000000
787
78.252000
1071
2430
1
chr6D.!!$R2
1359
11
TraesCS6A01G376900
chr6D
452639943
452642177
2234
True
239.600000
431
89.274000
794
2089
4
chr6D.!!$R3
1295
AutoCloner calculated primer pairs
These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
whilst remaining within the specified product range where possible.
Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
during PCR or sequencing,
these could be used as alternatives.